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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SNP analysis of human induced pluripotent stem cells

ABSTRACT: Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. However, the use of hIPSCs in the context of genetically inherited human disease will require correction of disease-causing mutations in a manner that is fully compatible with clinical applications. We analyzed hiPSC line and genetically modified derivatives using high-density SNP array to investigate genomic instability associated reprogramming and genetic modification. Primary iPSC lines derived from patients with alpha-1 antitrypsin deficiency were generated. This genetic disorder is caused by homozygous mutation (Glu342Lys) in the SERPINA1 gene. We carried out mutation correction by 2 steps: zinc-finger nuclease-stimuated gene targeting and piggyBac trasnsposon-mediated selection cassette elimination. Parental fibroblast lines, primary iPSC lines and homozygously targeted iPSC lines were subjected to SNP genotyping using Illumina CytoSNP-12 BeadChiP.

ORGANISM(S): Homo sapiens

SUBMITTER: Kosuke Yusa

PROVIDER: E-GEOD-31035 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SNP analysis of human induced pluripotent stem cells

Project description:Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. However, the use of hIPSCs in the context of genetically inherited human disease will require correction of disease-causing mutations in a manner that is fully compatible with clinical applications. We analyzed hiPSC line and genetically modified derivatives using high-density SNP array to investigate genomic instability associated reprogramming and genetic modification.

2011-09-01 | GSE31035 | GEO

CGH analyses of human induced pluripotent stem cells

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2013-08-04 | E-GEOD-43522 | biostudies-arrayexpress

SNP data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring G2019S mutations in the LRRK2 gene

Project description:We have generated human induced Pluripotent Stem cells (hiPSc) using Retroviral virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays. Gene expression profiling in patient-derived dopamine neurons identifies candidate therapeutic molecules in Parkinsonâs disease. human iPSc lines were derived from human dermal fibroblasts from 3 PD LRRK2 G2019S patients and 3 control donors. SNP and gene expression datasets were generated from patient and control lines. Note that iPS OX1-19 and iPS-NHDF-1, also used in the current study, have been published previously so datasets are not given here [GSE45472 PMID:23951090 ; GSE43904 PMID:24586273]

2016-02-09 | E-GEOD-77662 | biostudies-arrayexpress

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Project description:Human induced Pluripotent Stem cells (hiPSc) and their differentiated progeny have great potential for modelling disease. To realise this potential, robust protocols need to be developed for deriving authentic differentiated cell lineages and these lineages need to be rigorously characterised. We have generated hiPSc using retrovirus-mediated delivery of reprogramming factors, and have used them for characterising mid-brain dopaminergic neurons. hiPSc lines have been screened using SNP array to assess chromosomal stability, and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets. A mature physiological cellular model of human dopaminergic neurons. human iPSc lines were derived from normal human dermal fibroblasts.

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2015-08-03 | E-GEOD-69868 | biostudies-arrayexpress

Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells. [Agilent]

Project description:Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level. 22 samples: 1 human NPC, 2 human ESC (UNDIFF), 5 human iPSC (UNDIFF), 2 human ESC (EB_ecto), 5 human iPSC (EB_ecto), 2 human ESC (EB_mesend), 5 human iPSC (EB_mesend)

2014-01-01 | E-GEOD-51561 | biostudies-arrayexpress

Chromothripsis in AML

2013-08-04 | GSE43522 | GEO

SNP data from OX1 human fibroblasts and induced Pluripotent Stem cells

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2013-03-26 | E-GEOD-45471 | biostudies-arrayexpress

SNP data from human fibroblasts and induced Pluripotent Stem cells from Parkinson's Disease patients

Project description:We have generated human induced Pluripotent Stem cells (hiPSc) from Parkinson's Disease patients, using retrovirus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays. Fernandes H.J.R., Hartfield E.M., Badger J., Christian H. C., Emmanoulidou E., Vowles J., Evetts S., Vekrellis K., Talbot K., Hu M.T., James W., Cowley S.A., and Wade-Martins, R. Heterozygous glucocerebrosidase mutations in Parkinson's increase autophagic demand, but decrease capacity, in induced pluripotent stem cell-derived dopaminergic neuronal cultures. submitted for publication human iPSc lines were derived from human dermal fibroblasts from 2 Parkinson's Disease patients with heterozygous glucocerebrosidase mutations (GBA N370S) mutations, and 2 idiopathic Parkinson's Disease patients. SNP datasets from the 2 control individuals used in this study have been published previously [PMID 23951090; A mature physiological cellular model of human dopaminergic neurons Hartfield E.M., Yamasaki-Mann M., Fernandes H.J., Vowles., James W.S., Cowley S.A, and Wade-Martins R. In revision]

2013-12-18 | E-GEOD-53425 | biostudies-arrayexpress

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