Figure 1.

Schematic representation of the PASSPORT-seq assay. A pool of oligonucleotides flanking both alleles of 437 SNPs were cloned in parallel into the 3’UTR of the luciferase gene in pIS-0 vector. Colonies were pooled and DNA purified. The resulting plasmid library was transiently transfected into two neuroblastoma cells lines, SH-SY5Y and SK-N-BE(2). The cDNAs were synthesized from the total RNA. The target sequences were amplified from the cDNAs and the plasmid DNA extracted from the transfected cells using two step-PCR with unique barcodes for each cell line and each biological replicate. Following next-generation sequencing, the reads were aligned to the reference library consisting of all the test sequences and ASE was measured for each SNPs. ss = single-stranded; ds = double-stranded.