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An analysis fo genomic structural alterations in iPS cells derived from xeroderma pigmentosum patients

ABSTRACT: To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for iPS cells derived from xeroderma pigmentosum patients (XP3OS, XP40OS, and XPEMB-1). Samples were collected after 10 to 25 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher mutation rate of the iPS cells compared to those from normal cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE55520 | GEO | 2015/06/24

SECONDARY ACCESSION(S): PRJNA239827

REPOSITORIES: GEO

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An analysis fo genomic structural alterations in iPS cells derived from xeroderma pigmentosum patients

Project description:To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for iPS cells derived from xeroderma pigmentosum patients (XP3OS, XP40OS, and XPEMB-1). Samples were collected after 10 to 25 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher mutation rate of the iPS cells compared to those from normal cells. The iPS-cell samples were collected after several passages togerther with their precursor cell samples and subjected to the SNP genotyping array. We searched for structural mutations occurred during the culture of the iPS cells.

2015-06-24 | E-GEOD-55520 | biostudies-arrayexpress

An analysis of genomic structural alteration in three human ES cell lines.

Project description:To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for three human ES cell lines, namely, SEES-1, SEES-2, and SEES-3. Samples were collected after 4 to 60 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher genomic stability of the ES cells compared to some well-known normal cell lines.

2015-05-20 | GSE54576 | GEO

An analysis of genomic structural alteration in three human ES cell lines.

Project description:To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for three human ES cell lines, namely, SEES-1, SEES-2, and SEES-3. Samples were collected after 4 to 60 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher genomic stability of the ES cells compared to some well-known normal cell lines. Several samples were collected after 4 to 60 passages and subjected to the SNP genotyping array. We searched for structural mutations occurred during the culture of the ES cells.

2015-05-20 | E-GEOD-54576 | biostudies-arrayexpress

Genomic alteration in MRC5-derived induced pluripotent stem (MRC5-iPS) cell line, Tic

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

Homo sapiens

Project description:An analysis fo genomic structural alterations in iPS cells derived from xeroderma pigmentosum patients

| PRJNA239827 | ENA

Genomic alteration in MRC5-derived induced pluripotent stem (MRC5-iPS) cell line, Tic

2013-07-23 | GSE49082 | GEO

Homo sapiens

Project description:UVB light mutagenesis in Xeroderma Pigmentosum C human cells

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Homo sapiens

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Comparative transcriptomic analysis of WT and XP-C fibroblasts cultured in 3D-dermal equivalents

Project description:Xeroderma Pigmentosum (XP) is a rare autosomal genetic disease. XP patients present a default in the mechanism responsible for the repair of UV-induced DNA lesions. They are prone to develop skin cancers with high frequencies early in their life. To identify microenvironment factors that could contribute to the progression of skin cancers in XP-C group we did comparative transcriptomic analysis of WT and XP-C dermal patient’s fibroblasts.

2019-09-19 | GSE133084 | GEO

Fibroblast RNA-Seq data from three genodermatoses (RDEB, XPC and KS)

Project description:Recessive dystrophic epidermolysis bullosa, Kindler syndrome and xeroderma pigmentosum C, are three cancer-prone genodermatoses whose causal genetic mutations cannot fully explain, on their own, the array of associated phenotypic manifestations. Recent evidence highlights the contributing role of the stromal microenvironment in the pathology of these disorders. To investigate common mechanisms that contribute to the pathogenic role played by dermal fibroblasts, we conducted a comparative gene expression analysis by RNA-Seq.

2019-03-12 | GSE119501 | GEO

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