The genetic reprogramming technology allows generation of induced pluripotent stem cells (iPSCs) from somatic cells (Takahashi and Yamanaka, 2006) . iPSCs have the ability to self-renew, and to differentiate into any type of somatic cells, and are considered as a promising tool for drug development, disease modeling, and regenerative medicine. The reprogramming factors (oct4, sox2, klf4, c-myc) can be delivered to the cell nucleus either by vectors integrating into the genome (lentiviruses, r ...[more]
Project description:The paper reports data on measuring whole-genome DNA methylation using an Illumina 450K Methylation BeadChip platform for isogenic induced pluripotent stem cells (iPSCs) derived from fibroblasts of a healthy donor and a PARK-associated Parkinson's disease patient via integrating (lentiviral transfection) and non-integrating (Sendai virus infection) reprogramming. Data on whole-genome methylation of neurons generated by differentiation of the iPSCs were also presented. The iPSCs were reprogrammed using the four Yamanaka’s factors: OCT4 (POU5F1), SOX2, KLF4, and cMYC. The data evidence that there are no significant differences in whole-genome methylation of iPSCs produced by various methods. Overall design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina HumanMethylation450 BeadChip
Project description:Briefly, the well characterized female hES cell line H9 was allowed to differentiate into a clonally purified mortal splanchnopleuric mesodermal somatic cell line EN13. The EN13 line was subsequently virally reprogrammed back to an induced pluripotent state (we term re-H9) using OCT4, SOX2, KLF4 retroviral vectors creating isogenic lines of hESC, hiPSC and mortal cells. Our results reveal several important differences between embryo-derived H9 and the induced re-H9 stem cells. We find a dysregulation of genes involved in imprinting and altered expression of X-chromosome localized genes in re-H9 cells. 10 Samples. 1 hESC line, 6 isogenic hiPSC lines, 1 non-isogenic hiPSC line, 1 isogenic mortal line, 1 non-isogenic mortal line
Project description:Down syndrome (trisomy 21) is the most common genetic cause of intellectual disability, but the precise molecular mechanisms underlying impaired cognition remain unclear. Elucidation of these mechanisms has been hindered by the lack of a model system that contains full trisomy of chromosome 21 (Ts21) in a human genome that enables normal gene regulation. To overcome this limitation,we created Ts21-induced pluripotent stem cells (iPSCs) from two sets of Ts21 human fibroblasts. One of the fibroblast lines had low level mosaicism for Ts21 and yielded Ts21 iPSCs and an isogenic control that is disomic for human chromosome 21 (HSA21). Differentiation of all Ts21 iPSCs yielded similar numbers of neurons expressingmarkers characteristic of dorsal forebrain neurons that were functionally similar to controls. Expression profiling of Ts21 iPSCs and their neuronal derivatives revealed changes in HSA21 genes consistent with the presence of 50% more genetic material as well as changes in non- HSA21 genes that suggested compensatory responses to oxidative stress. Ts21 neurons displayed reduced synaptic activity, affecting excitatory and inhibitory synapses equally. Thus, Ts21 iPSCs and neurons display unique developmental defects that are consistent with cognitive deficits in individuals with Down syndrome and may enable discovery of the underlying causes of and treatments for this disorder. Three independent RNA samples were collected from Down syndrome (DS) and control iPSCs between passages 24 and 48. Three independent RNA samples were collected from 30 day old neurons differentiated from Down syndrome (DS) and control iPSCs.
Project description:We have generated isogenic induced pluripotent stem cell lines by reprogramming human fibroblasts from patients carrying the LRRK2 G2019S mutation with subsequent zinc finger nuclease - mediated targeted correction of the diseased allele. These iPS cell lines were differentiated for 30 days using a direct differentiation protocol towards midbrain dopaminergic neurons (mDANs). Isogenic human iPS cells carrying the LRRK2 WT and G2019S locus were differentiated to dopaminergic neurons to detect gene expression changes associated with mutated LRRK2.
Project description:Expression profiling of non coding RNAs using tilling arrays from ES, Fibroblasts and Fibroblasts derived iPSC LincRNA profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells Total RNA was extracted from human ESCs, fibroblast, and fibroblast-derived iPSC lines, then hybridized to Nimblegen tiling array GPL8791; Human lincRNA 364k Tiling Array V1
Project description:Expression profiling of non coding RNAs using tilling arrays from ES, Fibroblasts and Fibroblasts derived iPSC LincRNA profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells Overall design: Total RNA was extracted from human ESCs, fibroblast, and fibroblast-derived iPSC lines, then hybridized to Nimblegen tiling array GPL8791; Human lincRNA 364k Tiling Array V1
Project description:Human fibroblast-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express both cell surface markers and genes that characterize human embryonic stem (ES) cells. Keywords: Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells Overall design: After prolonged undifferentiated proliferation, these fibroblast-derived cells maintain the developmental potential to differentiate into derivatives of all three primary germ layers in both embryoid bodies and teratomas. These pluripotent cell lines were derived by the transduction of Oct4, Sox2, Nanog, and Lin28 into genetically unmodified, diploid human fibroblasts. Such human induced pluripotent cell lines should have broad applications in both the development of in vitro models of human disease and transplantation medicine.