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Mean DNA methylation levels of different genomic regions based on the genome-wide 450 K array data [AU ± SD]. AU, arbitrary unit; SD, standard deviation; hES, human embryonic stem cell; NSC, neural stem cell; iPS, induced pluripotent stem cell. (PDF 39 kb)

Table of analyzed single genes and primers. (PDF 40 kb)

DNA methylation levels of SNCA intron 1 in pluripotent stem cells (ESC line I3 and I6 (n = 1 each), iPSC line I3 (n = 3), ES- and iPS-NSC (line I3, n = 1 and n = 3, respectively), and ES- and iPS-Neurons (line I3, n = 1 and n = 3, respectively). ESC versus iPS-Neurons p = 0.03, iPSC vs. iPS-Neurons p = 0.02, and iPS-NSC vs. iPS-Neurons p = 0.02. (PDF 41 kb)

A–C Interindividual analysis of DMCG comparing hES-Neurons to each iPSC-derived neuronal clone. D X chromosomal-based DMCG analysis using Fisher’s test. Methylation deltas were calculated as indicated and CpGs above applying a moderate (0.2) or high (0.5) threshold. (PDF 437 kb)

Mean DNA methylation levels (%) of single genes (APP, GNAS, MIR886, PMP22, SNCA promoter, SNCA intron 1) of hESC-derived and iPSC-derived NSC and neurons. Analysis is based on individual samples. Data is shown as mean ± SD. (PDF 40 kb)

Comparison of mean Pearson DNA methylation correlation coefficients. Comparisons were made including all ESC- and iPSC-derived NSC and neurons from the human isogenic stem cell system (isogenic hESC- and iPSC-derived NSC and neurons), all samples from the study of Fernández-Santiago et al. [11] except fibroblasts, and all samples from the study of Kim et al. [15]. iPSC, induced pluripotent stem cell; LRRK2, leucin-rich repeat kinase 2; PD, Parkinson’s disease; iPD, idiopathic PD; DAn, dopaminergic neuron; n, number; NSC, neural stem cell; hES(C), human embryonic stem (cell); I3, ESC-line I3; H9, ESC-line H9. (PDF 49 kb)

A–C Immunocytochemical analysis of iPSC generated from hESC-derived NSC staining positive for the pluripotency-associated markers Oct4, Tra-1-60, and Tra-1-81. D–F Upon differentiation, these cells give rise to all three germ layers and express appropriate markers for endoderm (D; AFP), mesoderm (E, SMA), and ectoderm (F; TUBB3). G, H iPSC-derived NSC expressing the early neuroectodermal markers nestin, Dach1, ZO1, and PLZF. I, J 6-week-old iPSC-derived neurons staining for the neuronal marker MAP2 (I) and the neurotransmitter GABA (J). Nuclei are counterstained with DAPI. Scale bars: A–F, 75 μm; G–J, 10 μm. (PDF 3601 kb)