Investigation of Isogenic Human Embryonic Stem Cells and Derived Induced Pluripotent Stem Cells and Differentiated Line

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. [Expression profiling] 10 Samples: 1 hESC line, 6 isogenic hiPSC lines, 1 non-isogenic hiPSC line, 1 isogenic mortal line, 1 non-isogenic mortal line Supplementary file contains raw data. [Genome variation profiling] 6 Samples: 1 hESC line, 4 isogenic hiPSC lines, 1 isogenic mortal line. Supplementary file contains both raw and processed data (SNP genotype calls were made using the default parameters in Genome Studio and CNV calls were made using the default parameters of the CNV partition plugin in Genome Studio)the following columns for each SNP: Index, Name, Address, Chr, Position, GenTrain Score, Frac A, Frac C, Frac G, Frac T, and the following columns for each sample: GType, Score, Theta, R, X Raw, Y Raw, X, Y, B Allele Freq, Log R Ratio, Top Alleles