ABSTRACT: Female infertility syndromes are among the most prevalent chronic health disorders in women, but their molecular basis remains unknown because of the complexity of oogenesis and uncertainty regarding the number and identity of ovarian factors controlling the assembly, preservation, and maturation of ovarian follicles. To systematically discover such ovarian fertility factors en masse, we employed a mouse model (Foxo3), where follicles are assembled normally but are then synchronously activated. Gene expression profiling of mutant and normal ovaries led to the identification a surprisingly large set of ovarian factors. The set included the vast majority of known ovarian factors, many of which when mutated produce female sterility phenotypes, but most were novel. Subsequent analyses revealed novel classes of ovarian factors and significant overrpresentation on the X chromosome, among other insights into the general properties of oogenesis genes and their patterns of expression. Experiment Overall Design: Total ovarian RNA from +/+ and -/- ovaries at PND1, 3, 7, and 14 (n=3 replicates per timepoint and genotype, a total of 24 microarrays) was subjected to linear RNA amplification and hybridized to Affymetrix 430 2.0 mouse whole-genome microarrays, which interrogate >39K transcripts including the vast majority of protein-coding genes. We also profiled 14 somatic tissues. Additionally, to provide more refined views of gene expression, we profiled adult ovaries, adult testis, KitlSl/KitlSl-d testis (devoid of germ cells except for rare spermatogonia) (Shinohara et al., 2000), ES cells, laser-capture microdissected (LCM) primary oocytes, LCM somatic cells (granulosa cells + surrounding stroma), superovulated unfertilized eggs, cumulus granulosa cells, and E11 Foxo3 +/+ and -/- embryos. Each array data set was independently normalized by global median scaling, and the signal strengths were averaged for those samples for which replicates were available (PND1-14).
