Fibroblasts: grown in DMEM/FCS, brought to equivalent passage; iPSCs: grown in mTESR1 media on BD Matrigel; Neurons: differentiated according to the dual SMAD/ floor plate protocol, then enriched for dopaminergic neurons.
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was was extracted from blood, fibroblasts, iPS and neuralised iPS cell lines using the DNeasy Blood and Tissue Kit (Qiagen).
Label
C-Bio and A-DNP
Label protocol
200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
Hybridization protocol
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol
Beadchips were scanned using an iSscan(Illumina) with an AutoLoader (Illumina).
Description
Genomic DNA extracted from blood, fibroblasts, iPS and neuralised iPS cell lines was genotyped using HumanOmni1-Quad BeadChips (Illumina).
Data processing
Genomic DNA extracted from blood, fibroblasts, iPS and neuralised iPS cell lines was genotyped using and processed in GenomeStudio v1.8.X (Illumina) to generate SNP calls.
SNP data from genomic DNA from a subject, fibroblasts, iPSCs and neurons with four copies of SNCA, and genomic DNA from an unaffected first degree relative and equivalent cell lines
Expression and SNP data from fibroblasts, iPSCs and neurons with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative
