Fig. 1

SNP-based allele-specific ddPCR assays for ATXN3 transcript. a SCA3 cell lines used; R—reprogramming; D—differentiation. b Scheme of ATXN3 transcript with marked CAG repeat tract (green triangle) and SNP variants identified in SCA3 cell lines (red arrows—SNPs used in ddPCR assays; black arrows—other identified SNPs); light orange box—UTRs. Table presents all SNP variants identified in analyzed SCA3 cell lines. Bolded SNPs were selected to be targets for ddPCR assays, and they will be hereinafter referred to as ATXN3_SNP2 and ATXN3_SNP5 in the text. CDS—coding sequence. RefSNP number according to the Single Nucleotide Polymorphism Database (dbSNP). c Results from ddPCR analysis of ATXN3_SNP2 assay specificity performed on seven samples with predefined ratios of WT/MUT ATXN3 plasmids (samples: I—100% WT and 0% MUT; II—90% WT and 10% MUT; III—75% WT and 25% MUT; IV—50% WT and 50% MUT; V—25% WT and 75% MUT; VI—10% WT and 90% MUT; VII—0% WT and 100% MUT). Precise values are indicated on WT/MUT bars ± poisson error. d Percentage ratio of ATXN3 WT allele obtained with ddPCR ATXN3_SNP5 assay using gDNA from indicated SCA3 cell lines. Three biological replicates were performed. These data are presented as means ± SD