Human induced pluripotent stem cells (hiPSCs): gene expression and miRNA expression data

Induced pluripotent stem cells (iPSCs) outwardly appear to be indistinguishable from embryonic stem cells (ESCs). A study of gene expression profiles of mouse and human ESCs and iPSCs suggests that, while iPSCs are quite similar to their embryonic counterparts, a recurrent gene expression signature appears in iPSCs regardless of their origin or the method by which they were generated. Upon extended culture, hiPSCs adopt a gene expression profile more similar to hESCs; however, they still retain a gene expression signature unique from hESCs that extends to miRNA expression. Genome-wide data suggested that the iPSC signature gene expression differences are due to differential promoter binding by the reprogramming factors. High-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprogramming and that reprogramming does not lead to genomic instability. Together, these data suggest that iPSCs should be considered a unique subtype of pluripotent cell. Detailed analysis comparing induced pluripotent stem cells revealed functional gene expression differences to hESCs that are changed with long term passaging. We used microarrays to detail the changes that are made throughout passaging to hiPSC lines. Gene expression analysis: hiPSC lines were harvested at long term passages (p50-60) for RNA extraction and hybridization on Affymetrix arrays. miRNA expression analysis: Used a chip which comes with over 600 mature human miRNAs in quadruplicate. Two 40 mer oligo probes, one for the mature miRNA and the other for precursor oligo, are generally present, when possible from the sense strand of both arms of the hairpin structure of the microRNA precursor sequence collected from the Sanger Database.