PMC:1802744 / 2446-6043 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/1802744","sourcedb":"PMC","sourceid":"1802744","source_url":"http://www.ncbi.nlm.nih.gov/pmc/1802744","text":"Background\nModern DNA microarrays permit a comprehensive analysis of quantitative and qualitative changes in RNA transcript abundance, outlining the cross-sections of gene expression and alterations of these in response to genetic or environmental stimuli. Genome-scale microarrays (cDNA- or oligonucleotide-based) are most valuable when screening populations of cells for the novel genes reflecting potential diagnostic and prognostic markers or for an identification of novel therapeutic targets. On the other hand, custom microarray platforms that focus on specific pre-selected subset of genes relevant to a particular field of investigation can be less costly and more suitable for detection of smaller gene expression changes.\nMicroarray technology has added important information on both normal development and pathological changes in neurons. This is well illustrated by multiple studies on substantia nigra dopaminergic neurons, which degenerate in Parkinson's disease (PD) [1-5]. The shortcomings of pharmacological therapies in PD have stimulated a search for alternative treatment strategies. In successful cases, transplants of human embryonic mesencephalic dopaminergic neurons can both restore dopaminergic neurotransmission and provide some symptomatic relief [6-8]. A wider application of neural transplantation in PD is, however, currently not feasible due to the unpredictable and variable outcome, the risks of unwanted side-effects (dyskinesias) [9,10] and ethical and practical problems associated with using donor cells obtained from aborted embryos and fetuses [11,12]. Human embryonic stem cells (hESCs) are considered a promising future source of cells for cell replacement therapy in PD and other neurological conditions [13]. They could constitute a virtually infinite source of self-renewing cells that can be persuaded to differentiate into specific types of neural cells, including dopaminergic neurons [14-16]. The molecular mechanisms that govern development of cultured hESCs into specific types of neural cells are not fully understood. To promote our understanding of such mechanisms, it would be valuable to have tools that readily and reproducibly can help to characterize the cells as they differentiate from pluripotent stem cells into post-mitotic neurons. This important issue was addressed in earlier studies by Luo et al. and Yang et al., who designed small-to-moderate scale custom microarray platforms (281 and 755 gene targets, respectively) [17,18]. In addition SuperArray Bioscience Corporation (Frederick, MD, USA) have manufactured a range of small-scale arrays (263 gene targets for human array; [19]). We sought to create an improved and updated microarray platform for hESC/neuronal differentiation-oriented gene expression studies. Therefore, we generated a specialized large-scale DNA microarray platform (the \"NeuroStem Chip\") that has over 1,300 pre-selected gene targets and multiple controls spotted in quadruplicates (~46,000 spots total). Here we introduce the platform and the advantages it can offers to neuroscientists and stem cell biologists: particularly, in the niche of gene expression-oriented characterization of the samples using an assay of pre-selected, already established gene targets. In the current study, we use the NeuroStem Chip to characterize an undifferentiated population of pluripotent hESCs (cell line SA02, Cellartis AB, Göteborg, Sweden) and compare the gene expression in those cells with that of a hESC-derived cell population rich in neurons, including tyrosine hydroxylase-positive dopaminergic 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