Gene expression analysis of mouse F1 hybrids to study cis regulatory variations

To analyze the difference in gene expression between alleles of F1 hybrids of mouse C57BL6/J (B6) and MSM/Ms (MSM) strains, we sequenced these F1 hybrids of reciprocal crosses. While most genes did show allelic bias, a small number of genes showed either B6- or MSM-biaed expression in both crosses. These allelic differences were associated with the allelic differences in histone acetylation in promoter regions determined by another experiments. Using F1 hybrids between B6 and MSM of reciprocal crosses, RNA was extracted from female liver, and sequenced with the 150-bp paired-end mode. Alleles were determined for each read, and the allele frequencies were calculated for each gene. For each crosses, two biological replicates were analyzed.