To measure expression difference between the B and D alleles, we exploited transcribed SNPs to capture allelic expression difference in F1 hybrids [56] using a combination of RT-PCR and a single base extension technology (SNaPshot, Applied Biosystems, www.appliedbiosystems.com). For each transcript we analyzed, Primer 3 [110] was used to design a pair of PCR primers that target sequences on the same exon and flanking an informative SNP.
