Four pools of RNA from the hippocampus and four pools of genomic DNA from the spleen of F1 hybrids (male and female B6 × D2 F1 and D2 × B6 F1 hybrids) were prepared. To avoid contamination by genomic DNA, RNA pools were treated with Turbo DNase (Ambion, Austin, TX, USA), and then first strand cDNA was synthesized (GE Healthcare, Waukesha, WI, USA). The genomic DNA samples were used as controls, and both cDNA and genomic DNA samples were tested concurrently using the same assay to compare expression from the B and D alleles of Per3. We amplified the cDNA and genomic DNA using GoTaq Flexi DNA polymerase (Promega Corporation, www.promega.com). PCR products were purified using ExoSap-IT (USB Corporation, www.usbweb.com) followed by SNaPshot to extend primers by a single fluorescently labeled ddNTPs. Fluorescently labeled products were purified using calf intestinal phosphatase (CIP, New England BioLabs, Beverly, MA, USA) and separated by capillary electrophoresis on ABI3130 (Applied Biosystems, Foster City, CA, USA). Quantification was done using GeneMapper v4.0 software (Applied Biosystems), and transcript abundance was measured by peak intensities associated with
