RNAs isolated from ESC/iPSC, NSCs, and dopaminergic populations were hybridized to Illumina Human HT-12 BeadChip (Illumina, Inc., San Diego, CA; performed by Microarray core facility at the Burnham Institute for Medical Research). Array data processing and analysis was performed using Illumina BeadStudio software. The Illumina array data were normalized by the background method. The maximum expression value for probe set of one gene was chosen as the expression value of this gene. Using the processed data, we conducted Global array clustering of genes across all the hESC/iPSC, NSC, and dopaminergic samples, using the complete linkage method and measuring the Euclidean distance. The result was presented by a dendrogram. Differentially expressed gene was defined if the gene showed twofold expression change between any two samples. The data of differentially expressed genes were transformed to log2 signal values for each gene across all samples. Unsupervised two-way hierarchical clustering of differentially expressed genes was analyzed with The Institute for Genomic Research Multiexperiments Viewer (MEV) v4.5.1 [13], which used complete linkage and Euclidean distance metric to generate the hierarchical tree. High expressions relative to
