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Chunk #11 — Materials and Methods — Allele-specific expression (ASE)

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Cis-regulatory variants affect CHRNA5 mRNA expression in populations of African and European ancestry.
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used for rs16969968 pre-amplification are: forward primer 5′-CGCCTTTGGTCCGCAAGATA-3′ and reverse primer 5′-TGCTGATGGGGGAAGGTGGAG-3′. Primers used for rs615470 pre-amplification are: forward primer 5′- CAGATGATCCATTTGAACAGTTGGC-3′ and reverse primer 5′- TAGAGACGGGGTTTCTCCACGTTG-3′. Portions of pre-amplified cDNA from heterozygous samples for rs16969968 and/or rs615470 were arrayed in triplicate onto 384-well plates. As a control, a portion of pre-amplified gDNA from matched samples was also arrayed in duplicate onto the same 384-well plate. All reactions were evaluated on an ABI-7900HT Fast real-time PCR system under standard conditions.