Effects of naturally ocurring proto-Y chromosomes on house fly gene expression

We performed RNA-seq experiments to examine the effects of house fly proto-Y chromosomes on gene expression. Two different Y^M chromosomes were investigated, and two different III^M chromosomes were investigated. One of the Y^M genotypes also was also heterozygous for third chromosomes that do not carry a male-determining locus to evaluate the effect of third chromosomes on gene expression independent of being a proto-Y. Four different genotypes were assayed. For each genotype, expression was measured in both head and abdomen. Three biological replicates of each genotype and tissue were assayed.