Germline-biased gene expression in transformed ovaries. (a) Heat diagram (yellow > red > blue) of hybridization intensities for all unique array element sequences (N = 13,267) from individual samples (columns) used in this study. Gonad samples (left) and somatic samples (right) are indicated with karyotype (XX;AA and X;AA) and abbreviated genotypes; wt, wild type (see Materials and methods for more details). Replicates are indicated (brackets). Germline expression is clearly evident in the gene-expression profiles of transformed ovaries. There are large blocks of elements showing high- or low-intensity hybridization to gonad probes and the opposite pattern when hybridized to samples from carcasses or from flies lacking germ cells but having somatic components of the gonads. (b) Selected genes with known functions in the germline. Array elements representing germline-marker genes (for example, vasa (vas), pumilio (pum), tudor (tud), piwi and benign gonial cell neoplasia (bgcn) [67,68]) show strong hybridization to labeled gonad mRNA samples and comparatively weaker hybridization to non-germline samples. Furthermore, at least some of the differences between the samples also support the proposed germline sex-determination pathway. For example, as predicted, both ovo and otu are germline-biased and overexpressed in XX;AA Sxl ovaries relative to X;AA hs-tra ovaries [40,69]. All these data validate the use of XX;AA and X;AA transformed germlines as matched tissues for the careful analysis of X-chromosome dosage compensation in the germline.