Additional Supporting Information may be found in the online version of this article.

SC_11-0388_sm_SuppTable1.pdf98KSupplementary Table 1
SC_11-0388_sm_SuppTable2.pdf96KSupplementary Table 2
SC_11-0388_sm_SuppTable3.pdf121KSupplementary Table 3
SC_11-0388_sm_SupplInform.pdf103KSupporting Information
SC_11-0388_sm_supplFigure1.tif2278KSupporting Information Figure S1. Neuronal differentiation and characterization of iPSCs that are derived from a Huntington's disease patient (HD-iPSC). (A): Experimental scheme showing a step-wise differentiation procedure. (B): Neural rosette-like structures formed through co-culturing HDiPSC with PA6 stromal cells (Stage 3, see the text for details). Arrow indicates a representative neural rosette-like structure. (C): Neurospheres formed though suspension culture of isolated neural rosette-like structures (Stage 4). (D): Neural precursor cells undergoing expansion as single cells (Stage 5-NP), which were made by dissociation of neurospheres using accutase. (E): Differentiated neuronal cells formed from the attached neurospheres (Stage 5-MN).
SC_11-0388_sm_supplFigure2.tif2445KSupporting Information Figure S2. Analyses of chromosomal changes and CAG repeat number changes in HD-iPSC. (A): Karyotypic analysis showing normal chromosome morphology and numbers after extensive expansion or neuronal differentiation of HD-iPSC (same results). (B): Genomic DNA PCR analysis showing no changes of CAG repeat numbers (i.e., 72 repeats) after extensive expansion (i.e., 62 more passages from passage 11 to passage 73) of HD-iPS cells. Arrow indicates the mutant huntingtin allele. No additional band was detected from hESC after extensive expansion (i.e., 73 more passages from passage 36 to passage 109) or normal control. CAG repeat numbers were counted by sequencing. (C): Genomic DNA PCR analysis showing no changes of CAG repeat numbers after neuronal differentiation of HD-iPSC. Arrow indicates the mutant huntingtin allele. No additional band was detected after neuronal differentiation of hESC. CAG repeat numbers were counted as above. Note that HD gene is highly polymorphic and father and mother may carry different numbers of CAG repeats, which will result in different sizes of PCR bands, as shown in (B) and (C).
SC_11-0388_sm_supplFigure3.tif595KSupporting Information Figure S3. Comparison of neuronal differentiation efficiency in H9, F5, HD and HD2 cells, in conjunction with transgene expression. (A): Histogram showing the percentage of rosette-forming colonies out of total colonies at Stage 3. (B): Percentage of neural forming area in each colony at Stage 3. (C): Real-time qPCR results showing the relative endogenous mRNA expression levels of four Yamanaka factors (Oct4, Sox2, Klf4 and c-Myc) in H9, F5, HD and HD2 cells. Expression levels of each gene were adjusted to those in H9 cells. Note the relatively strong expression of Klf4 gene in F5 and HD2 cells. (D): Real-time qPCR results showing the relative expression levels of Sox2 transgene at Stage 5-NP. Results are shown in a log scale. Note the low level of Sox2 transgene expression in HD cells.

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