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. Overall design: 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.